
Hello all, turns out i'm having a bad R week.  I am at my wits end with a function that I am trying to write.  When I run the lines of code outside of a function, I get the desired output.  When I wrap the lines of code into a function it doesn't work as expected.  Not sure what is going on here.  I suspected that the syntax of the if statement with the for loop was the culprit, but when I only ran the part of the code with the for loop with no if statement I still had the above problem (works outside function, fails when wrapped into a function).  Below is the code and example output.  Please help!  

 

         Thanks, 

                 Aaron

 

concov.test<-function(vegetation,specieslist)
{
 test.veg<-vegetation
 names(test.veg)<-specieslist$LifeForm
 tmp<-matrix(nrow=nrow(test.veg),ncol=length(unique(names(test.veg))))
 for (i in unique(names(test.veg))) {test.out<-apply(test.veg[,names(test.veg)==i],1,sum)
  tmp.match<-unique(names(test.veg))[unique(names(test.veg))==i]
  tmp.col<-match(tmp.match,unique(names(test.veg)))
  tmp[1:nrow(test.veg),tmp.col]<-test.out
  tmp.out<-data.frame(row.names(test.veg),tmp,row.names=1);names(tmp.out)<-unique(names(test.veg))
  tmp.out
  tmp.out.sort<-tmp.out[,order(names(tmp.out))]
 }
 if(table(names(tmp.out))[i]==1)
  tmp.match2<-names(tmp.out.sort)[names(tmp.out.sort)==i]
  tmp.col2<-match(tmp.match2,names(tmp.out.sort))
  tmp.out.sort[1:nrow(test.veg),tmp.col2]<-test.veg[,names(test.veg)==i]
         return(tmp.out.sort)
 else return(tmp.out.sort)
}

 

----Incorrect output when run as function-----

 

> test<-concov.test(ansveg_all,spplist.class)
> test
                        Bare_Ground Deciduous_Shrubs Deciduous_Tree Evergreen_Shrubs Evergreen_Tree Forbs Grasses Lichens Mosses Sedges
ANSG_T01_01_2008          NA               NA             NA               NA             NA    NA      NA      NA   95.0     NA
ANSG_T01_02_2008          NA               NA             NA               NA             NA    NA      NA      NA   16.0     NA
ANSG_T01_03_2008          NA               NA             NA               NA             NA    NA      NA      NA   71.0     NA
ANSG_T01_04_2008          NA               NA             NA               NA             NA    NA      NA      NA   10.0     NA
ANSG_T02_01_2008          NA               NA             NA               NA             NA    NA      NA      NA   92.2     NA
ANSG_T02_02_2008          NA               NA             NA               NA             NA    NA      NA      NA   14.0     NA

.

.

.

 

----Correct output when code is run outside of a function----

 

> test.veg<-ansveg_all
> names(test.veg)<-spplist.class$LifeForm
> tmp<-matrix(nrow=nrow(test.veg),ncol=length(unique(names(test.veg))))
> 
> for (i in unique(names(test.veg))) {test.out<-apply(test.veg[,names(test.veg)==i],1,sum)
+ tmp.match<-unique(names(test.veg))[unique(names(test.veg))==i]
+ tmp.col<-match(tmp.match,unique(names(test.veg)))
+ tmp[1:nrow(test.veg),tmp.col]<-test.out
+ tmp.out<-data.frame(row.names(test.veg),tmp,row.names=1);names(tmp.out)<-unique(names(test.veg))
+ tmp.out
+ tmp.out.sort<-tmp.out[,order(names(tmp.out))]
+ }
> if(table(names(tmp.out))[i]==1)
+ tmp.match2<-names(tmp.out.sort)[names(tmp.out.sort)==i]
> tmp.col2<-match(tmp.match2,names(tmp.out.sort))
> tmp.out.sort[1:nrow(test.veg),tmp.col2]<-test.veg[,names(test.veg)==i]
>         return(tmp.out.sort)
> else return(tmp.out.sort)
> 
> 
> tmp.out.sort
                 Bare_Ground Deciduous_Shrubs Deciduous_Tree Evergreen_Shrubs Evergreen_Tree Forbs Grasses Lichens Mosses Sedges
ANSG_T01_01_2008           0             57.0            1.0             40.0           35.0  22.0     5.0    35.0   95.0    1.1
ANSG_T01_02_2008           0              0.0            0.0              0.0            0.0  34.0     0.0     0.0   16.0   24.0
ANSG_T01_03_2008           0             31.0            0.0             47.0            1.0   9.1     3.0     3.0   71.0   14.0
ANSG_T01_04_2008           0              0.0            0.0             12.0            0.0  13.2     0.0     0.0   10.0   16.0
ANSG_T02_01_2008           0             15.0            1.0             22.0           36.0   9.2     2.0    38.0   92.2    0.1
ANSG_T02_02_2008           0             33.0           66.0             23.0            2.0   5.0     0.0     3.0   14.0    0.0
.

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